You can change the default settings in three ways:
Figure 1. Exploring the Settings Perspective
Once you have edited the schema with your ideal settings, save it by clicking on Save As in the bottom-left corner, give it a name and click OK (see Figure 2). Now you will see your custom schema listed under Schemas. Unlike the BGS Factory Settings (default) schema, created schemas can be removed and edited.
Figure 2. Saving and naming the new schema
When you start an analysis in the Analysis Perspective (Monitor in QuiC), you can change the default settings in the Experiment Setup window (see Figure 3). For each aspect of the analysis, you can choose your preferred settings. Click Finish when the experiment has been configured. In this case, the changes will only apply to the ongoing analysis and won’t be saved for future setups.
In the Analysis Perspective, right click on the experiment tab and choose Settings. Additionally, in Spectronaut software you can find convenient icons that comprise shortcut to settings and other analysis functions (Figure 4). Now, at the bottom half of the window, you can see the Analysis Settings (Figure 5). Similarly, to point number 2, for each aspect of the analysis, you can choose your preferred settings. Click Confirm to start recalculating.
Figure 4. Changing the settings to an already analyzed
Figure 5. Choosing your preferred settings to recalculate the analysis